eventOutcomeCompare {SPLINTER} | R Documentation

## eventOutcomeCompare

### Description

Compares two sequences and gives differences if there's a switch from 1->2 if seq2 is NULL, assume seq1 is a list of length 2 to compare

### Usage

    eventOutcomeCompare(seq1, seq2 = NULL, genome, direction = TRUE,
      fullseq = TRUE, verbose = FALSE)

### Arguments

`seq1` | GRangesList
`seq2` | GRangesList
`genome` | BSGenome object
`direction` | logical. Report direction of sequence change.
`fullseq` | logical. Report full sequences.
`verbose` | logical. turn messages on/off.

### Value

list containing
(1) tt : PairwiseAlignmentsSingleSubject pairwise alignment
(2) eventtypes : string detailing primary event classification

### Author(s)

Diana LOW

### Examples

    suppressMessages(library(BSgenome.Mmusculus.UCSC.mm9))
    bsgenome<-BSgenome.Mmusculus.UCSC.mm9
    eventOutcomeCompare(seq1=compatible_cds$hits[[1]],seq2=region_minus_exon,
     genome=bsgenome,direction=TRUE)

[Package SPLINTER version 1.8.1 Index]